[gmx-users] Interaction energy..

[rama david]

Hi,
 I got the result by g_energy.
Thank you for these .

but when I used g_enemat with the edr file ( out put from mdrun -rerun )
g_enemat -f ener.edr -groups groups.dat
i got following out put

roup 0WARNING! could not find group (null):extra34-extra34 (0,0)in energy
file
WARNING! could not find group Coul-SR:extra34-energy (0,1)in energy file
WARNING! could not find group LJ-SR:extra34-energy (0,1)in energy file
WARNING! could not find group (null):extra34-energy (0,1)in energy file
group 1WARNING! could not find group (null):energy-energy (1,1)in energy
file

Will select half-matrix of energies with 4 elements
Last energy frame read 50000 time 10000.000
Will build energy half-matrix of 2 groups, 4 elements, over 50001 frames
Segmentation fault (core dumped)

i used the following groups.dat file

2
extra34
energy


What is reason for the error ?? Is I did any mistake again??

Thank you in advance.


With best wishes and regards,

Rama david


On Fri, Oct 5, 2012 at 10:32 PM, rama david <ramadavidgroup at gmail.com>wrote:

> Hi justin,
> Ok now I get
> I have to modify mdp parameter ..
>
> Thank you,
> With best wishes and regards,
> Rama david
>
> On Fri, Oct 5, 2012 at 9:47 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 10/5/12 11:46 AM, rama david wrote:
>>
>>> Thank you for your Help.
>>>
>>> I did the following tc-groups
>>>
>>> tcoupl        = V-rescale    ; modified Berendsen thermostat
>>> tc-grps        =  extra34 Non-Protein energy    ; two coupling groups -
>>> more accurate
>>> tau_t        = 0.1    0.1 0.1        ; time constant, in ps
>>> ref_t        =  310    310 310     ; reference temperature, one for each
>>> group, in K
>>> ;
>>>
>>> Energy contain the residues that i needed
>>> extra34 contain all the remaining ligand and receptor atom
>>> non-protein contain sol and ion.
>>>
>>> I got the energy file after mdrun -rerun
>>>
>>> I used the g_energy term
>>>
>>> It give me the following output
>>> End your selection with an empty line or a zero.
>>> ------------------------------**------------------------------**-------
>>>    1  G96Angle         2  Proper-Dih.      3  Improper-Dih.    4
>>> LJ-14
>>>    5  Coulomb-14       6  LJ-(SR)          7  LJ-(LR)          8
>>> Disper.-corr.
>>>    9  Coulomb-(SR)    10  Coul.-recip.    11  Potential       12
>>> Kinetic-En.
>>>   13  Total-Energy    14  Temperature     15  Pres.-DC        16
>>> Pressure
>>>   17  Constr.-rmsd    18  Box-X           19  Box-Y           20
>>> Box-Z
>>>   21  Volume          22  Density         23  pV              24
>>> Enthalpy
>>>   25  Vir-XX          26  Vir-XY          27  Vir-XZ          28
>>> Vir-YX
>>>   29  Vir-YY          30  Vir-YZ          31  Vir-ZX          32
>>> Vir-ZY
>>>   33  Vir-ZZ          34  Pres-XX         35  Pres-XY         36
>>> Pres-XZ
>>>   37  Pres-YX         38  Pres-YY         39  Pres-YZ         40
>>> Pres-ZX
>>>   41  Pres-ZY         42  Pres-ZZ         43  #Surf*SurfTen   44
>>> Box-Vel-XX
>>>   45  Box-Vel-YY      46  Box-Vel-ZZ      47  Mu-X            48
>>> Mu-Y
>>>   49  Mu-Z            50  T-extra34       51  T-non-Protein   52
>>> T-energy
>>>   53  Lamb-extra34                        54
>>> Lamb-non-Protein
>>>   55  Lamb-energy
>>>
>>>
>>> So I confused. though it shows the energy group, which option should i
>>> have
>>> to choose ??
>>>
>>> What is Lamb-energy???
>>>
>>>
>> It is related to temperature coupling.
>>
>>
>>  Is I did any mistake??? or I have to use any else command ??
>>>
>>>
>> I have told you to use "energygrps" (which is described in the manual)
>> and you're specifying "tc-grps."  Temperature coupling and energy
>> calculation groups are very different concepts.
>>
>>
>> -Justin
>>
>> --
>> ==============================**==========
>>
>> Justin A. Lemkul, Ph.D.
>> Research Scientist
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>>
>> ==============================**==========
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